get counts by gene for single cell rna seq

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3.1 years ago

das2000sidd ▴ 30

Hi

I have just got started with single cell RNA seq and I have two queries. One is how do I combine my dataset and an externally downloaded dataset for subsequent dimension reduction usage such as UMAP? I have the matrix, barcode and features file for both the datasets.

How do I get count by gene from a single cell RNA from the object read using Seurat? If count_data was an object read in by Read10X of Seurat object, then I see I can access the genes using count_data@Dimnames[[1]] and the count matrix using count_data@meta.data. But I am not sure how to get the counts by gene.

Any help would be much appreciated.

Thanks!

scRNA-seq single-cell • 2.6k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 3.1 years ago by das2000sidd ▴ 30

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Hi, can you confirm that you read https://satijalab.org/seurat/articles/essential_commands.html and then say where you get stuck?

ADD REPLY • link 3.1 years ago by ATpoint 82k

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